Interface for Substitution models, defined as a mixture of "simple" substitution models. More...

#include <Bpp/Phyl/Model/MixedSubstitutionModel.h>

Inheritance diagram for bpp::MixedSubstitutionModel:

Collaboration diagram for bpp::MixedSubstitutionModel:

Public Member Functions
	MixedSubstitutionModel ()

virtual	~MixedSubstitutionModel ()

virtual MixedSubstitutionModel *	clone () const =0

virtual const SubstitutionModel *	getNModel (size_t i) const =0
	Returns a specific model from the mixture. More...

virtual SubstitutionModel *	getNModel (size_t i)=0

virtual double	getNProbability (size_t i) const =0
	Returns the probability of a specific model from the mixture. More...

virtual const std::vector< double > &	getProbabilities () const =0

virtual void	setNProbability (size_t i, double prob)=0
	Sets the probability of a specific model from the mixture. More...

virtual size_t	getNumberOfModels () const =0

virtual const std::vector< double > &	getVRates () const =0
	Returns the rates of the submodels. More...

virtual double	getNRate (size_t i) const =0
	Returns the rate of a specific submodel. More...

virtual void	setVRates (const Vdouble &vd)=0
	Sets the rates of the submodels to be proportional to a given vector, and normalizes them so that the mean rate of the mixture equals rate_. More...

virtual void	normalizeVRates ()=0
	Normalizes the rates of the submodels so that the mean rate of the mixture equals rate_. More...

virtual Vint	getSubmodelNumbers (std::string &desc) const =0

virtual std::string	getName () const =0
	Get the name of the model. More...

virtual const std::vector< int > &	getAlphabetStates () const =0

virtual const StateMap &	getStateMap () const =0

virtual std::vector< size_t >	getModelStates (int code) const =0
	Get the state in the model corresponding to a particular state in the alphabet. More...

virtual std::vector< size_t >	getModelStates (const std::string &code) const =0
	Get the state in the model corresponding to a particular state in the alphabet. More...

virtual int	getAlphabetStateAsInt (size_t index) const =0

virtual std::string	getAlphabetStateAsChar (size_t index) const =0

virtual double	freq (size_t i) const =0

virtual double	Qij (size_t i, size_t j) const =0

virtual double	Pij_t (size_t i, size_t j, double t) const =0

virtual double	dPij_dt (size_t i, size_t j, double t) const =0

virtual double	d2Pij_dt2 (size_t i, size_t j, double t) const =0

virtual const Vdouble &	getFrequencies () const =0

virtual const Matrix< double > &	getGenerator () const =0

virtual const Matrix< double > &	getExchangeabilityMatrix () const =0

virtual double	Sij (size_t i, size_t j) const =0

virtual const Matrix< double > &	getPij_t (double t) const =0

virtual const Matrix< double > &	getdPij_dt (double t) const =0

virtual const Matrix< double > &	getd2Pij_dt2 (double t) const =0

virtual void	enableEigenDecomposition (bool yn)=0
	Set if eigenValues and Vectors must be computed. More...

virtual bool	enableEigenDecomposition ()=0
	Tell if eigenValues and Vectors must be computed. More...

virtual const Vdouble &	getEigenValues () const =0

virtual const Vdouble &	getIEigenValues () const =0

virtual bool	isDiagonalizable () const =0

virtual bool	isNonSingular () const =0

virtual const Matrix< double > &	getRowLeftEigenVectors () const =0

virtual const Matrix< double > &	getColumnRightEigenVectors () const =0

virtual const Alphabet *	getAlphabet () const =0

virtual size_t	getNumberOfStates () const =0
	Get the number of states. More...

virtual double	getInitValue (size_t i, int state) const =0 throw (IndexOutOfBoundsException, BadIntException)

virtual double	getScale () const =0
	Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale. More...

virtual void	setScale (double scale)=0
	Multiplies the current generator by the given scale. More...

virtual double	getRate () const =0
	Get the rate. More...

virtual void	setRate (double rate)=0
	Set the rate of the model (must be positive). More...

virtual void	addRateParameter ()=0

virtual void	setFreqFromData (const SequenceContainer &data, double pseudoCount=0)=0
	Set equilibrium frequencies equal to the frequencies estimated from the data. More...

virtual void	setFreq (std::map< int, double > &frequencies)
	Set equilibrium frequencies. More...

virtual const FrequenciesSet *	getFrequenciesSet () const
	If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0. More...

Detailed Description

Interface for Substitution models, defined as a mixture of "simple" substitution models.

Author: Laurent Guéguen

Definition at line 59 of file MixedSubstitutionModel.h.

Constructor & Destructor Documentation

◆ MixedSubstitutionModel()

bpp::MixedSubstitutionModel::MixedSubstitutionModel ( )

inline

Definition at line 63 of file MixedSubstitutionModel.h.

◆ ~MixedSubstitutionModel()

virtual bpp::MixedSubstitutionModel::~MixedSubstitutionModel ( )

inlinevirtual

Definition at line 65 of file MixedSubstitutionModel.h.

Member Function Documentation

◆ addRateParameter()

virtual void bpp::SubstitutionModel::addRateParameter ( )

pure virtualinherited

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::G2001, and bpp::TS98.

Referenced by bpp::AbstractBiblioSubstitutionModel::addRateParameter().

◆ clone()

virtual MixedSubstitutionModel* bpp::MixedSubstitutionModel::clone ( ) const

pure virtual

Implements bpp::SubstitutionModel.

Implemented in bpp::MixtureOfSubstitutionModels, bpp::MixtureOfASubstitutionModel, bpp::LLG08_EX3, bpp::LLG08_EHO, bpp::LLG08_UL3, bpp::LG10_EX_EHO, bpp::LGL08_CAT, bpp::LLG08_EX2, bpp::LLG08_UL2, bpp::AbstractMixedSubstitutionModel, bpp::YNGKP_M1, bpp::YNGKP_M8, bpp::YNGKP_M7, bpp::YNGKP_M3, bpp::YNGKP_M2, and bpp::AbstractBiblioMixedSubstitutionModel.

◆ d2Pij_dt2()

virtual double bpp::SubstitutionModel::d2Pij_dt2	(	size_t	i,
		size_t	j,
		double	t
	)		const

pure virtualinherited

Returns: The second order derivative of the probability of change from state i to state j with respect to time t, at time t.

See also: getd2Pij_dt2(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::d2Pij_dt2().

◆ dPij_dt()

virtual double bpp::SubstitutionModel::dPij_dt	(	size_t	i,
		size_t	j,
		double	t
	)		const

pure virtualinherited

Returns: The first order derivative of the probability of change from state i to state j with respect to time t, at time t.

See also: getdPij_dt(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::dPij_dt().

◆ enableEigenDecomposition() [1/2]

virtual void bpp::SubstitutionModel::enableEigenDecomposition ( bool yn )

pure virtualinherited

Set if eigenValues and Vectors must be computed.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition(), and bpp::YpR::YpR().

◆ enableEigenDecomposition() [2/2]

virtual bool bpp::SubstitutionModel::enableEigenDecomposition ( )

pure virtualinherited

Tell if eigenValues and Vectors must be computed.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

◆ freq()

virtual double bpp::SubstitutionModel::freq ( size_t i ) const

pure virtualinherited

Returns: Equilibrium frequency associated to character i.

See also: getFrequencies(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::TwoTreeLikelihood::computeTreeD2Likelihood(), bpp::TwoTreeLikelihood::computeTreeDLikelihood(), and bpp::AbstractBiblioSubstitutionModel::freq().

◆ getAlphabet()

virtual const Alphabet* bpp::SubstitutionModel::getAlphabet ( ) const

pure virtualinherited

Returns: Get the alphabet associated to this model.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AAExteriorSubstitutionRegister::AAExteriorSubstitutionRegister(), bpp::AAInteriorSubstitutionRegister::AAInteriorSubstitutionRegister(), bpp::SubstitutionModelSet::addModel(), bpp::DecompositionReward::alphabetIndexHasChanged(), bpp::ComprehensiveSubstitutionRegister::ComprehensiveSubstitutionRegister(), bpp::DecompositionReward::DecompositionReward(), bpp::DecompositionSubstitutionCount::DecompositionSubstitutionCount(), bpp::AbstractMutationProcess::detailedEvolve(), bpp::LaplaceSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::AbstractSubstitutionRegister::getAlphabet(), bpp::AbstractBiblioSubstitutionModel::getAlphabet(), bpp::MarkovModulatedSubstitutionModel::getAlphabet(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::DnDsSubstitutionRegister::getType(), bpp::SelectedSubstitutionRegister::SelectedSubstitutionRegister(), bpp::CategorySubstitutionRegister::setCategories(), bpp::LaplaceSubstitutionCount::setSubstitutionModel(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::DecompositionSubstitutionCount::setSubstitutionModel(), bpp::DecompositionReward::setSubstitutionModel(), bpp::UniformizationSubstitutionCount::substitutionRegisterHasChanged(), bpp::DecompositionSubstitutionCount::substitutionRegisterHasChanged(), bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount(), bpp::YpR::updateMatrices(), and bpp::BppOSubstitutionModelFormat::writeMixed_().

◆ getAlphabetStateAsChar()

virtual std::string bpp::SubstitutionModel::getAlphabetStateAsChar ( size_t index ) const

pure virtualinherited

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getAlphabetStateAsChar(), bpp::TwoTreeLikelihood::getAlphabetStateAsChar(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsChar(), and bpp::SubstitutionModelSet::getAlphabetStateAsChar().

◆ getAlphabetStateAsInt()

virtual int bpp::SubstitutionModel::getAlphabetStateAsInt ( size_t index ) const

pure virtualinherited

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getAlphabetStateAsInt(), bpp::TwoTreeLikelihood::getAlphabetStateAsInt(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsInt(), bpp::SubstitutionModelSet::getAlphabetStateAsInt(), bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(), bpp::CategorySubstitutionRegister::getCategory(), bpp::SiteSimulationResult::getSite(), bpp::CategorySubstitutionRegister::getType(), bpp::TsTvSubstitutionRegister::getType(), bpp::DnDsSubstitutionRegister::getType(), bpp::GCSynonymousSubstitutionRegister::getType(), and bpp::NonHomogeneousSequenceSimulator::multipleEvolve().

◆ getAlphabetStates()

virtual const std::vector<int>& bpp::SubstitutionModel::getAlphabetStates ( ) const

pure virtualinherited

Returns: The alphabet states of each state of the model, as a vector of int codes.

See also: Alphabet

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::DecompositionReward::computeBMatrice_(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::AbstractBiblioSubstitutionModel::getAlphabetStates(), bpp::TwoTreeLikelihood::getAlphabetStates(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStates(), bpp::SubstitutionModelSet::getAlphabetStates(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::CategorySubstitutionRegister::setCategories(), bpp::NaiveSubstitutionCount::setSubstitutionModel(), and bpp::LabelSubstitutionCount::setSubstitutionModel().

◆ getColumnRightEigenVectors()

virtual const Matrix<double>& bpp::SubstitutionModel::getColumnRightEigenVectors ( ) const

pure virtualinherited

Returns: A matrix with right eigen vectors. Each column in the matrix stands for an eigen vector.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::DecompositionReward::computeEigen_(), bpp::AbstractBiblioSubstitutionModel::getColumnRightEigenVectors(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

◆ getd2Pij_dt2()

virtual const Matrix<double>& bpp::SubstitutionModel::getd2Pij_dt2 ( double t ) const

pure virtualinherited

Returns: All second order derivatives of the probability of change from state i to state j with respect to time t, at time t.

See also: d2Pij_dt2()

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::AbstractBiblioSubstitutionModel, and bpp::WordSubstitutionModel.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::fireParameterChanged(), and bpp::AbstractBiblioSubstitutionModel::getd2Pij_dt2().

◆ getdPij_dt()

virtual const Matrix<double>& bpp::SubstitutionModel::getdPij_dt ( double t ) const

pure virtualinherited

Returns: Get all first order derivatives of the probability of change from state i to state j with respect to time t, at time t.

See also: dPij_dt()

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::AbstractBiblioSubstitutionModel, and bpp::WordSubstitutionModel.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::fireParameterChanged(), and bpp::AbstractBiblioSubstitutionModel::getdPij_dt().

◆ getEigenValues()

virtual const Vdouble& bpp::SubstitutionModel::getEigenValues ( ) const

pure virtualinherited

Returns: A vector with all real parts of the eigen values of the generator of this model;

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::DecompositionReward::computeEigen_(), bpp::AbstractBiblioSubstitutionModel::getEigenValues(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

◆ getExchangeabilityMatrix()

virtual const Matrix<double>& bpp::SubstitutionModel::getExchangeabilityMatrix ( ) const

pure virtualinherited

Returns: The matrix of exchangeability terms. It is recommended that exchangeability matrix be normalized so that the normalized generator be obtained directly by the dot product $S . \pi$ .

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::Coala::Coala(), bpp::AbstractBiblioSubstitutionModel::getExchangeabilityMatrix(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

◆ getFrequencies()

virtual const Vdouble& bpp::SubstitutionModel::getFrequencies ( ) const

pure virtualinherited

Returns: A vector of all equilibrium frequencies.

See also: freq()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::TwoTreeLikelihood::computeTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::AbstractBiblioSubstitutionModel::getFrequencies(), bpp::TwoTreeLikelihood::getRootFrequencies(), bpp::AbstractHomogeneousTreeLikelihood::getRootFrequencies(), bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

◆ getFrequenciesSet()

virtual const FrequenciesSet* bpp::SubstitutionModel::getFrequenciesSet ( ) const

inlinevirtualinherited

If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.

Reimplemented in bpp::JCprot, bpp::AbstractBiblioSubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::DSO78, bpp::JTT92, bpp::LG08, bpp::YNGKP_M1, bpp::YNGKP_M8, bpp::YNGKP_M7, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::YNGKP_M3, bpp::YNGKP_M2, and bpp::AbstractCodonFrequenciesSubstitutionModel.

Definition at line 479 of file SubstitutionModel.h.

Referenced by bpp::AbstractBiblioSubstitutionModel::getFrequenciesSet(), and bpp::BppOSubstitutionModelFormat::write().

◆ getGenerator()

virtual const Matrix<double>& bpp::SubstitutionModel::getGenerator ( ) const

pure virtualinherited

Returns: The normalized Markov generator matrix, i.e. all normalized rates of changes from state i to state j. The generator is normalized so that (i) $\forall i; \sum_j Q_{i,j} = 0$ , meaning that $ $\forall i; Q_{i,i} = -\sum_{j \neq i}Q_{i,j}$ , and (ii) $\sum_i Q_{i,i} \times \pi_i = -1$ . This means that, under normalization, the mean rate of replacement at equilibrium is 1 and that time are measured in units of expected number of changes per site. Additionnaly, the rate_ attibute provides the possibility to increase or decrease this mean rate.

See Kosiol and Goldman (2005), Molecular Biology And Evolution 22(2) 193-9.

See also: Qij()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::LaplaceSubstitutionCount::computeCounts(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::AbstractBiblioSubstitutionModel::getGenerator(), bpp::SimpleMutationProcess::SimpleMutationProcess(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

◆ getIEigenValues()

virtual const Vdouble& bpp::SubstitutionModel::getIEigenValues ( ) const

pure virtualinherited

Returns: A vector with all imaginary parts of the eigen values of the generator of this model;

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getIEigenValues().

◆ getInitValue()

virtual double bpp::SubstitutionModel::getInitValue	(	size_t	i,
		int	state
	)		const
throw	(	IndexOutOfBoundsException,
		BadIntException
	)

pure virtualinherited

This method is used to initialize likelihoods in reccursions. It typically sends 1 if i = state, 0 otherwise, where i is one of the possible states of the alphabet allowed in the model and state is the observed state in the considered sequence/site.

Parameters

i	the index of the state in the model.
state	An observed state in the sequence/site.

Returns: 1 or 0 depending if the two states are compatible.

Exceptions

IndexOutOfBoundsException	if array position is out of range.
BadIntException	if states are not allowed in the associated alphabet.

See also: getStates();

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getInitValue().

◆ getModelStates() [1/2]

virtual std::vector<size_t> bpp::SubstitutionModel::getModelStates ( int code ) const

pure virtualinherited

Get the state in the model corresponding to a particular state in the alphabet.

Parameters

code	The alphabet state to check.

Returns: A vector of indices of model states.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getModelStates(), bpp::SubstitutionModelSet::getModelStates(), and bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates().

◆ getModelStates() [2/2]

virtual std::vector<size_t> bpp::SubstitutionModel::getModelStates ( const std::string & code ) const

pure virtualinherited

Get the state in the model corresponding to a particular state in the alphabet.

Parameters

code	The alphabet state to check.

Returns: A vector of indices of model states.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

◆ getName()

virtual std::string bpp::SubstitutionModel::getName ( ) const

pure virtualinherited

Get the name of the model.

Returns: The name of this model.

Referenced by bpp::AbstractCodonFitnessSubstitutionModel::AbstractCodonFitnessSubstitutionModel(), bpp::AbstractSubstitutionModel::fireParameterChanged(), bpp::MixtureOfSubstitutionModels::getSubmodelNumbers(), bpp::BppOSubstitutionModelFormat::readMixed_(), bpp::AbstractBiblioSubstitutionModel::updateMatrices(), and bpp::BppOSubstitutionModelFormat::write().

◆ getNModel() [1/2]

virtual const SubstitutionModel* bpp::MixedSubstitutionModel::getNModel ( size_t i ) const

pure virtual

Returns a specific model from the mixture.

Implemented in bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioMixedSubstitutionModel.

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(), bpp::RHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractBiblioMixedSubstitutionModel::getNModel(), and bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood().

◆ getNModel() [2/2]

virtual SubstitutionModel* bpp::MixedSubstitutionModel::getNModel ( size_t i )

pure virtual

Implemented in bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioMixedSubstitutionModel.

◆ getNProbability()

virtual double bpp::MixedSubstitutionModel::getNProbability ( size_t i ) const

pure virtual

Returns the probability of a specific model from the mixture.

Implemented in bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioMixedSubstitutionModel.

Referenced by bpp::MixedSubstitutionModelSet::computeHyperNodesProbabilities(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(), bpp::MixedSubstitutionModelSet::getHyperNodeProbability(), bpp::AbstractBiblioMixedSubstitutionModel::getNProbability(), and bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood().

◆ getNRate()

virtual double bpp::MixedSubstitutionModel::getNRate ( size_t i ) const

pure virtual

Returns the rate of a specific submodel.

Implemented in bpp::AbstractBiblioMixedSubstitutionModel, and bpp::AbstractMixedSubstitutionModel.

Referenced by bpp::AbstractBiblioMixedSubstitutionModel::getNRate().

◆ getNumberOfModels()

virtual size_t bpp::MixedSubstitutionModel::getNumberOfModels ( ) const

pure virtual

Implemented in bpp::AbstractBiblioMixedSubstitutionModel, and bpp::AbstractMixedSubstitutionModel.

Referenced by bpp::MixedSubstitutionModelSet::complete(), bpp::SubstitutionModelSetTools::createNonHomogeneousModelSet(), bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(), bpp::RHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractBiblioMixedSubstitutionModel::getNumberOfModels(), bpp::BppOSubstitutionModelFormat::readMixed_(), and bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood().

◆ getNumberOfStates()

virtual size_t bpp::SubstitutionModel::getNumberOfStates ( ) const

pure virtualinherited

Get the number of states.

For most models, this equals the size of the alphabet.

See also: getAlphabetChars for the list of supported states.

Returns: The number of different states in the model.

Implemented in bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::YpR, bpp::AbstractBiblioSubstitutionModel, bpp::AbstractWordSubstitutionModel, bpp::BinarySubstitutionModel, bpp::gBGC, bpp::NucleotideSubstitutionModel, and bpp::ProteinSubstitutionModel.

Referenced by bpp::SubstitutionModelSet::addModel(), bpp::OneJumpSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::TwoTreeLikelihood::getNumberOfStates(), bpp::AbstractBiblioSubstitutionModel::getNumberOfStates(), bpp::AbstractHomogeneousTreeLikelihood::getNumberOfStates(), bpp::BranchLikelihood::initModel(), bpp::RE08::RE08(), bpp::SimpleMutationProcess::SimpleMutationProcess(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

◆ getPij_t()

virtual const Matrix<double>& bpp::SubstitutionModel::getPij_t ( double t ) const

pure virtualinherited

Returns: All probabilities of change from state i to state j during time t.

See also: Pij_t()

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::AbstractBiblioSubstitutionModel, and bpp::WordSubstitutionModel.

Referenced by bpp::LaplaceSubstitutionCount::computeCounts(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::computeCounts_(), bpp::DecompositionReward::computeRewards_(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::OneJumpSubstitutionCount::getAllNumbersOfSubstitutions(), and bpp::AbstractBiblioSubstitutionModel::getPij_t().

◆ getProbabilities()

virtual const std::vector<double>& bpp::MixedSubstitutionModel::getProbabilities ( ) const

pure virtual

Implemented in bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioMixedSubstitutionModel.

Referenced by bpp::RHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousMixedTreeLikelihood::fireParameterChanged(), and bpp::AbstractBiblioMixedSubstitutionModel::getProbabilities().

◆ getRate()

virtual double bpp::SubstitutionModel::getRate ( ) const

pure virtualinherited

Get the rate.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::G2001, and bpp::TS98.

Referenced by bpp::AbstractBiblioSubstitutionModel::getRate(), and bpp::MarkovModulatedSubstitutionModel::getRate().

◆ getRowLeftEigenVectors()

virtual const Matrix<double>& bpp::SubstitutionModel::getRowLeftEigenVectors ( ) const

pure virtualinherited

Returns: A matrix with left eigen vectors. Each row in the matrix stands for an eigen vector.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::DecompositionReward::computeEigen_(), and bpp::AbstractBiblioSubstitutionModel::getRowLeftEigenVectors().

◆ getScale()

virtual double bpp::SubstitutionModel::getScale ( ) const

pure virtualinherited

Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.

Returns: Minus the scalar product of diagonal elements and the frequencies vector.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getScale().

◆ getStateMap()

virtual const StateMap& bpp::SubstitutionModel::getStateMap ( ) const

pure virtualinherited

Returns: The mapping of model states with alphabet states.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getStateMap(), bpp::SubstitutionModelSet::getStateMap(), and bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator().

◆ getSubmodelNumbers()

virtual Vint bpp::MixedSubstitutionModel::getSubmodelNumbers ( std::string & desc ) const

pure virtual

Implemented in bpp::MixtureOfSubstitutionModels, bpp::AbstractBiblioMixedSubstitutionModel, and bpp::MixtureOfASubstitutionModel.

Referenced by bpp::PhylogeneticsApplicationTools::completeMixedSubstitutionModelSet(), and bpp::AbstractBiblioMixedSubstitutionModel::getSubmodelNumbers().

◆ getVRates()

virtual const std::vector<double>& bpp::MixedSubstitutionModel::getVRates ( ) const

pure virtual

Returns the rates of the submodels.

Implemented in bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioMixedSubstitutionModel.

Referenced by bpp::AbstractBiblioMixedSubstitutionModel::getVRates().

◆ isDiagonalizable()

virtual bool bpp::SubstitutionModel::isDiagonalizable ( ) const

pure virtualinherited

Returns: True if the model is diagonalizable in R.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::isDiagonalizable().

◆ isNonSingular()

virtual bool bpp::SubstitutionModel::isNonSingular ( ) const

pure virtualinherited

Returns: True is the model is non-singular.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::isNonSingular().

◆ normalizeVRates()

virtual void bpp::MixedSubstitutionModel::normalizeVRates ( )

pure virtual

Normalizes the rates of the submodels so that the mean rate of the mixture equals rate_.

Implemented in bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioMixedSubstitutionModel.

Referenced by bpp::MixedSubstitutionModelSet::computeHyperNodesProbabilities(), and bpp::AbstractBiblioMixedSubstitutionModel::normalizeVRates().

◆ Pij_t()

virtual double bpp::SubstitutionModel::Pij_t	(	size_t	i,
		size_t	j,
		double	t
	)		const

pure virtualinherited

Returns: The probability of change from state i to state j during time t.

See also: getPij_t(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::SimpleMutationProcess::evolve(), bpp::OneJumpSubstitutionCount::getNumberOfSubstitutions(), and bpp::AbstractBiblioSubstitutionModel::Pij_t().

◆ Qij()

virtual double bpp::SubstitutionModel::Qij	(	size_t	i,
		size_t	j
	)		const

pure virtualinherited

Returns: The rate in the generator of change from state i to state j.

See also: getStates();

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::UniformizationSubstitutionCount::fillBMatrices_(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::SubstitutionMappingTools::getNormalizationsPerBranch(), bpp::AbstractMutationProcess::getTimeBeforeNextMutationEvent(), bpp::AbstractBiblioSubstitutionModel::Qij(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::SimpleMutationProcess::SimpleMutationProcess(), bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount(), and bpp::YpR::updateMatrices().

◆ setFreq()

virtual void bpp::SubstitutionModel::setFreq ( std::map< int, double > & frequencies )

inlinevirtualinherited

Set equilibrium frequencies.

Parameters

frequencies The map of the frequencies to use.

Definition at line 473 of file SubstitutionModel.h.

Referenced by bpp::AbstractBiblioSubstitutionModel::setFreq().

◆ setFreqFromData()

virtual void bpp::SubstitutionModel::setFreqFromData	(	const SequenceContainer &	data,
		double	pseudoCount = `0`
	)

pure virtualinherited

Set equilibrium frequencies equal to the frequencies estimated from the data.

Parameters

data	The sequences to use.
pseudoCount	A quantity $\psi$ to add to adjust the observed values in order to prevent issues due to missing states on small data set. The corrected frequencies shall be computed as $\pi_i = \frac{n_i+\psi}{\sum_j (f_j+\psi)}$

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::JCprot, bpp::K80, bpp::RE08, bpp::JCnuc, bpp::UserProteinSubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::WAG01, bpp::DSO78, bpp::JTT92, bpp::LG08, and bpp::Coala.

Referenced by bpp::BppOSubstitutionModelFormat::read(), bpp::AbstractBiblioSubstitutionModel::setFreqFromData(), and bpp::MarkovModulatedSubstitutionModel::setFreqFromData().

◆ setNProbability()

virtual void bpp::MixedSubstitutionModel::setNProbability	(	size_t	i,
		double	prob
	)

pure virtual

Sets the probability of a specific model from the mixture.

Implemented in bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioMixedSubstitutionModel.

Referenced by bpp::MixedSubstitutionModelSet::computeHyperNodesProbabilities(), and bpp::AbstractBiblioMixedSubstitutionModel::setNProbability().

◆ setRate()

virtual void bpp::SubstitutionModel::setRate ( double rate )

pure virtualinherited

Set the rate of the model (must be positive).

Parameters

rate	must be positive.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::AbstractBiblioSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::G2001, and bpp::TS98.

Referenced by bpp::AbstractBiblioSubstitutionModel::setRate(), and bpp::MarkovModulatedSubstitutionModel::setRate().

◆ setScale()

virtual void bpp::SubstitutionModel::setScale ( double scale )

pure virtualinherited

Multiplies the current generator by the given scale.

Parameters

scale the scale by which the generator is multiplied.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::setScale(), and bpp::MarkovModulatedSubstitutionModel::setScale().

◆ setVRates()

virtual void bpp::MixedSubstitutionModel::setVRates ( const Vdouble & vd )

pure virtual

Sets the rates of the submodels to be proportional to a given vector, and normalizes them so that the mean rate of the mixture equals rate_.

Parameters

vd	a vector of positive values such that the rates of the respective submodels are in the same proportions (ie this vector does not need to be normalized).

Implemented in bpp::MixtureOfSubstitutionModels, bpp::AbstractMixedSubstitutionModel, and bpp::AbstractBiblioMixedSubstitutionModel.

Referenced by bpp::AbstractBiblioMixedSubstitutionModel::setVRates().

◆ Sij()

virtual double bpp::SubstitutionModel::Sij	(	size_t	i,
		size_t	j
	)		const

pure virtualinherited

Returns: The exchangeability between state i and state j.

By definition Sij(i,j) = Sij(j,i).

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::Sij().

The documentation for this class was generated from the following file:

Bpp/Phyl/Model/MixedSubstitutionModel.h

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ MixedSubstitutionModel()

◆ ~MixedSubstitutionModel()

Member Function Documentation

◆ addRateParameter()

◆ clone()

◆ d2Pij_dt2()

◆ dPij_dt()

◆ enableEigenDecomposition() [1/2]

◆ enableEigenDecomposition() [2/2]

◆ freq()

◆ getAlphabet()

◆ getAlphabetStateAsChar()

◆ getAlphabetStateAsInt()

◆ getAlphabetStates()

◆ getColumnRightEigenVectors()

◆ getd2Pij_dt2()

◆ getdPij_dt()

◆ getEigenValues()

◆ getExchangeabilityMatrix()

◆ getFrequencies()

◆ getFrequenciesSet()

◆ getGenerator()

◆ getIEigenValues()

◆ getInitValue()

◆ getModelStates() [1/2]

◆ getModelStates() [2/2]

◆ getName()

◆ getNModel() [1/2]

◆ getNModel() [2/2]

◆ getNProbability()

◆ getNRate()

◆ getNumberOfModels()

◆ getNumberOfStates()

◆ getPij_t()

◆ getProbabilities()

◆ getRate()

◆ getRowLeftEigenVectors()

◆ getScale()

◆ getStateMap()

◆ getSubmodelNumbers()

◆ getVRates()

◆ isDiagonalizable()

◆ isNonSingular()

◆ normalizeVRates()

◆ Pij_t()

◆ Qij()

◆ setFreq()

◆ setFreqFromData()

◆ setNProbability()

◆ setRate()

◆ setScale()

◆ setVRates()

◆ Sij()